Single-cell Analysis of Host-Microbiome Interactions

Installation

Here, we use pak to install package, you can also use remotes

if (!requireNamespace("pak")) {
    install.packages("pak",
        repos = sprintf(
            "https://r-lib.github.io/p/pak/devel/%s/%s/%s",
            .Platform$pkgType, R.Version()$os, R.Version()$arch
        )
    )
}

rsahmi depends on polars, you can install it by:

if (Sys.info()["sysname"] == "Linux") {
    pak::pkg_install(
        "https://github.com/pola-rs/r-polars/releases/latest/download/polars__x86_64-pc-linux-gnu.gz"
    )
} else if (Sys.info()["sysname"] == "Darwin") {
    pak::pkg_install(
        "https://github.com/pola-rs/r-polars/releases/latest/download/polars__x86_64-apple-darwin20.tgz"
    )
} else {
    stop("Unsupported operating system")
}

You can also install the development version of polars from Github or R-universe:

In this way, you must install rustc to compile polars, you can install rustc with rustup:

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh

Then install the polars package:

pak::pkg_install("pola-rs/r-polars")

Or

pak::repo_add("https://community.r-multiverse.org")
pak::pkg_install("polars")

Then you can install rsahmi:

pak::pkg_install("Yunuuuu/rsahmi")

You must also install seqkit and kraken2.

Cite

If you use this package, please cite:

• Ghaddar B, Biswas A, Harris C, Omary MB, Carpizo DR, Blaser MJ, De S. Tumor microbiome links cellular programs and immunity in pancreatic cancer. Cancer Cell. 2022 Oct 10;40(10):1240-1253.e5. doi: 10.1016/j.ccell.2022.09.009. PMID: 36220074; PMCID: PMC9556978.
• Ghaddar B, Blaser MJ, De S. Denoising sparse microbial signals from single-cell sequencing of mammalian host tissues. Nat Comput Sci. 2023 Sep;3(9):741-747. doi: 10.1038/s43588-023-00507-1. Epub 2023 Sep 18. PMID: 37946872; PMCID: PMC10634611.
• Song, Yuxuan PhD; Peng, Yun PhD; Qin, Caipeng PhD; Jiang, Shan PhD; Lin, Jiaxing PhD; Lai, Shicong MD; Wu, Jilin PhD; Ding, Mengting PhD; Du, Yiqing PhD*; Yu, Luping MD*; Xu, Tao MD*. Antibiotic use attenuates response to immune checkpoint blockade in urothelial carcinoma via inhibiting CD74-MIF/COPA: revealing cross-talk between anti-bacterial immunity and ant-itumor immunity. International Journal of Surgery 111(1):p 972-987, January 2025. | DOI: 10.1097/JS9.0000000000001901